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9988c2b
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@JuliaRegistrator register
Release notes:
New Features
Creating PEtabODEProblem with default options
Based on our benchmark paper, we now automatically select a gradient method, Hessian method, and ODE solver based on the problem (e.g. number of model parameters) if the user does not provide any options. Thus if a
PEtabODEProblem
is created viaa
PEtabODEProblem
with options that are likely to perform well specific model is created.Additional features for PEtabODEProblem
Via the
PEtabODEProblem
we can now in addition to previously supported methods compute:gradient = petabProblem.computeGradient(θ)
hessian = petabProblem.computeHessian(θ)
chi2 = petabProblem.computeChi2(θ)
simulatedValues = petabProblem.computeSimulatedValues(θ)
residuals = petabProblem.computeHessian(θ)
Defining the Model Directly in Julia Instead of via SBML
By the PEtab standard, the ODE model should be defined in the SBML format. However, sometimes it can be easier to write the model directly in Julia. Thus, we have added support for directly defining the model in the
ModelingToolkit.jl
format. Guidelines on how to formulate the model can be found in the documentation under Providing the model as a Julia file instead of a SBML File.Breaking Changes
The following functions have been replaced/renamed:
setupPEtabODEProblem
has been replaced withcreatePEtabODEProblem
. UnlikesetupPEtabODEProblem
,createPEtabODEProblem
only takes one required argument (the petab-model). Any other options are provided via keywords, so to set an ODE solver, for example, provide the following:getODESolverOptions
has been replaced by directly calling a constructor method forODESolverOptions
. To create anODESolverOptions
struct, simply call:getSteadyStateSolverOptions
has been replaced by directly calling a constructor method forSteadyStateSolverOptions
. To create aSteadyStateSolverOptions
struct, simply call:Since this package is young, breaking changes like these occur. However, we aspire to keep breaking changes to a minimum, and we appreciate users patience.
Other Changes
9988c2b
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Registration pull request updated: JuliaRegistries/General/83301
After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.
This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via: